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(-) Description

Title :  CRYSTAL STRUCTURE OF XENAVIDIN
 
Authors :  S. H. Helppolainen, J. A. E. Maatta, T. T. Airenne, M. S. Johnson, M. S. Ku H. R. Nordlund
Date :  20 Apr 07  (Deposition) - 27 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,D
Biol. Unit 1:  A,D  (2x)
Keywords :  Avidin, Beta-Barrel, Biotin-Binding Protein, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. A. E. Maatta, S. H. Helppolainen, V. P. Hytonen, M. S. Johnson, M. S. Kulomaa, T. T. Airenne, H. R. Nordlund
Structural And Functional Characteristics Of Xenavidin, The First Frog Avidin From Xenopus Tropicalis.
Bmc Struct. Biol. V. 9 63 2009
PubMed-ID: 19788720  |  Reference-DOI: 10.1186/1472-6807-9-63

(-) Compounds

Molecule 1 - XENAVIDIN
    Chains: A, D
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Common: FALL ARMYWORM
    Expression System Vector Type: BACULOVIRUS
    Organism Common: WESTERN CLAWED FROG
    Organism Scientific: XENOPUS TROPICALIS
    Organism Taxid: 8364

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AD
Biological Unit 1 (2x): AD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
1BTN2Ligand/IonBIOTIN
2FMT10Ligand/IonFORMIC ACID
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1BTN4Ligand/IonBIOTIN
2FMT20Ligand/IonFORMIC ACID

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN A:14 , LEU A:16 , SER A:18 , TYR A:35 , THR A:37 , VAL A:39 , SER A:40 , LEU A:41 , TRP A:69 , SER A:72 , SER A:74 , THR A:76 , TRP A:96 , ASN A:117 , HOH A:2066 , TRP D:109BINDING SITE FOR RESIDUE BTN A1123
02AC2SOFTWARETRP A:109 , ASN D:14 , LEU D:16 , SER D:18 , TYR D:35 , THR D:37 , VAL D:39 , SER D:40 , LEU D:41 , TRP D:69 , SER D:72 , SER D:74 , THR D:76 , TRP D:96 , ASN D:117 , HOH D:2045 , HOH D:2111BINDING SITE FOR RESIDUE BTN D1124
03AC3SOFTWAREASN D:14 , LYS D:15 , ALA D:116 , ASN D:117 , THR D:118 , HOH D:2112 , HOH D:2113BINDING SITE FOR RESIDUE FMT D1125
04AC4SOFTWAREASN A:14 , LYS A:15 , ALA A:116 , ASN A:117 , THR A:118 , HOH A:2096 , HOH A:2099BINDING SITE FOR RESIDUE FMT A1124
05AC5SOFTWAREHIS A:68 , LEU D:57 , HOH D:2115 , HOH D:2116BINDING SITE FOR RESIDUE FMT D1126
06AC6SOFTWARESER D:100 , GLN D:102 , ARG D:113 , HOH D:2117 , HOH D:2118BINDING SITE FOR RESIDUE FMT D1127
07AC7SOFTWAREGLU A:105 , GLN A:106 , ASN A:108 , TRP A:109 , HOH A:2100 , HOH A:2101 , LEU D:16BINDING SITE FOR RESIDUE FMT A1125
08AC8SOFTWAREGLY A:115 , ALA A:116 , HOH A:2074 , HOH A:2104 , HOH A:2105 , HOH A:2106BINDING SITE FOR RESIDUE FMT A1128
09AC9SOFTWARESER D:24 , VAL D:25 , SER D:26 , GLU D:30 , PHE D:31BINDING SITE FOR RESIDUE FMT D1128
10BC1SOFTWARELEU A:16 , GLU D:105 , GLN D:106 , ASN D:108 , TRP D:109 , HOH D:2097BINDING SITE FOR RESIDUE FMT D1129
11BC2SOFTWAREVAL A:39 , SER A:40 , THR A:42 , HOH A:2102 , HOH D:2099BINDING SITE FOR RESIDUE FMT A1126
12BC3SOFTWARESER A:100 , GLN A:102 , ARG A:113 , HOH A:2093 , HOH A:2103BINDING SITE FOR RESIDUE FMT A1127

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:6 -A:82
2D:6 -D:82

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2UYW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2UYW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2UYW)

(-) Exons   (0, 0)

(no "Exon" information available for 2UYW)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:119
 aligned with A7YYL1_XENTR | A7YYL1 from UniProtKB/TrEMBL  Length:148

    Alignment length:119
                                    31        41        51        61        71        81        91       101       111       121       131         
         A7YYL1_XENTR    22 QKCNLQGQWRNKLGSNLIIESVSQNGEFTGTYFTSVSLTNSTIRISPLTGYQKLTEKPTFGFTVHWAFSDSITVWTGQCFLNEKGEEILHTMWLLRSSQEKEQDNWTGTRVGGNTFTRL 140
               SCOP domains d2uywa_ A: automated matches                                                                                            SCOP domains
               CATH domains 2uywA00 A:4-122  [code=2.40.128.30, no name defined]                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee....eeee.......eeeeeee............eeeeeee......eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 2uyw A   4 QKCNLQGQWRNKLGSNLIIESVSQNGEFTGTYFTSVSLTNSTIRISPLTGYQKLTEKPTFGFTVHWAFSDSITVWTGQCFLNEKGEEILHTMWLLRSSQEKEQDNWTGTRVGANTFTRL 122
                                    13        23        33        43        53        63        73        83        93       103       113         


Chain D from PDB  Type:PROTEIN  Length:119
 aligned with A7YYL1_XENTR | A7YYL1 from UniProtKB/TrEMBL  Length:148

    Alignment length:119
                                    32        42        52        62        72        82        92       102       112       122       132         
         A7YYL1_XENTR    23 KCNLQGQWRNKLGSNLIIESVSQNGEFTGTYFTSVSLTNSTIRISPLTGYQKLTEKPTFGFTVHWAFSDSITVWTGQCFLNEKGEEILHTMWLLRSSQEKEQDNWTGTRVGGNTFTRLS 141
               SCOP domains d2uywd_ D: automated matches                                                                                            SCOP domains
               CATH domains 2uywD00 D:5-123  [code=2.40.128.30, no name defined]                                                                    CATH domains
           Pfam domains (1) -Avidin-2uywD01 D:6-121                                                                                              -- Pfam domains (1)
           Pfam domains (2) -Avidin-2uywD02 D:6-121                                                                                              -- Pfam domains (2)
         Sec.struct. author .....eeeee....eeeeeee....eeeeeee............eeeeeee......eeeeeee......eeeeeeeeee.....eeeeeeeeee....hhhhhhh.eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 2uyw D   5 KCNLQGQWRNKLGSNLIIESVSQNGEFTGTYFTSVSLTNSTIRISPLTGYQKLTEKPTFGFTVHWAFSDSITVWTGQCFLNEKGEEILHTMWLLRSSQEKEQDNWTGTRVGANTFTRLS 123
                                    14        24        34        44        54        64        74        84        94       104       114
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: Avidin] (113)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2UYW)

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